This repository contains notebooks for analyzing a Xenium In Situ dataset from a human breast cancer FFPE section.
The dataset used in this analysis is the Xenium In Situ dataset from a 0.4 cm² human breast cancer FFPE section, provided by 10x Genomics. It was downloaded from:
The direct download link for the dataset is:
To reproduce the analysis, download the dataset from the link above and extract it to the same location.
Analyze_Xenium_data.ipynb: Main analysis notebook for the Xenium dataset.
To run the analysis, you need to set up a Python environment with the required dependencies. There are two options:
This file contains the exact environment specification, including all dependencies.
- Clone this repository:
git clone https://github.com/BulutHamali/xenium-analysis-clean.git cd xenium-analysis-clean - Create a conda environment using environment.yml
conda env create -f environment.yml conda activate xenium_env
- Run the notebook in JupyterLab:
jupyter lab
This file lists the key dependencies, which can be installed with pip.
-
Clone this repository (as above).
-
Create a conda environment and install dependencies:
conda create -n xenium_env python=3.9 conda activate xenium_env pip install -r requirements.txt
-
Run the notebook in JupyterLab (as above).
You can choose whether to include the environment.yml file in the repository for full reproducibility or ignore it if requirements.txt is sufficient.
Add and commit the environment.yml file, then update the README.md with the instructions above.
git add environment.yml README.md
git commit -m "Add environment.yml and update README with instructions"
git pushIf you don’t want to include environment.yml in the repository (e.g., because requirements.txt is sufficient), you can add it to .gitignore to prevent Git from tracking it.
-
Add
environment.ymlto.gitignore:echo "environment.yml" >> .gitignore
Remove the file from your directory if you don’t need it:
rm environment.yml
Add and commit the updated
.gitignore:git add .gitignore git commit -m "Update .gitignore to ignore environment.yml" git push
This project is licensed under the MIT License - see the file for details.